Chapter 03:
When Sonic and Shadow arrived to Robotropolis, they were greeted with a horrifying sight: the city itself, which had been half destroyed when Sonic took out Robotnik, was back up and running, with SWATbots marching about, patrolling the edge of the city. Shadow and Sonic ducked down behind a wall and Shadow hissed to Sonic. “And you said you took out Robotnik the other day? What's going on?”
Sonic shook his head. “Honestly I have no idea. This shouldn't even be possible!”
Shadow and Sonic peeked out from the side of the wall to see if the area was clear, only to duck back when a unit of Combots marched by. Once the sound of marching metal faded, Shadow peeked back around, eyeing the citadel in the distance. “Maybe we'd better go check and see who else is home, if you know what I mean.”
Sonic nodded in agreement, looking around to see if the coast was clear. “Follow me.”
He darted off, with Shadow to catch up and follow him. Dodging additional SWATbot patrols and Combot units, the two hedgehogs made their way towards the large, oval shaped citadel in the distance. Sonic lead Shadow to an outer air duct system and pulled off the grate. “Through here.”
Shadow began to crawl inside, with Sonic following in, closing the grate behind them. “Just head straight for a while, I'll give you directions to Robuttnik's old control room.”
“Right.” Shadow murmured and began to crawl ahead, listening to Sonic's directions. As they got closer, Shadow thought he could hear a sound...a familiar voice. High pitched, weasely in tone. It was mostly laughing, but every once in a while, he thought he heard a command such as 'Go run another patrol.' or 'Bring me another drink!'. His eyes narrowed and he looked back to Sonic. “Is that who I think it is?”
Sonic's eyes also narrowed. “Snively,” he concluded. “I should of known. He must have been hiding from the explosion after the Annihilator was destroyed.” 
Shadow nodded as he stopped just outside the grate leading down into the control room. Down below, Snively was sitting in Robotnik's old chair, sipping on a glass of what looked to be a fizzy lemonade with a small cocktail umbrella. He was watching old security videos of Sonic beating the crap out of Robotnik, having a good laugh, especially moments when Robotnik was particularly humiliated.
Shadow and Sonic looked up to each other and nodded in mutual understanding.
Snively practically jumped and screeched in a high pitched voice when the grate from overhead was kicked out, dropping to the ground with a clang. The two hedgehogs jumped down, and Shadow was to first grab Snively by the collar and lift him up. “Alright you little toadie! You got some things to answer for!”
Sonic pressed in near Snively as he squealed in fear. “Yeah like how you were able to get Robotropolis running again so fast!”
Snively tried to stutter in an apparent show of trying, and failing miserably, to be furious. “H-how dare you come in here! SWA-”
Shadow slammed the little man against his chair and used his other hand to grasp the few hairs on his nearly bald head. “Call the SWATbots and you can inherit your uncle's completely hairless scalp!”
Snively squeeled in sheer terror. “NO NO! Not that!!! Anything but that!!!”
Sonic leaned in again. “Then start talking. How did you get the city up and running so fast?”
Snively began sweating, stuttering. “A-after you and the big round guy had the big fight, I-I took off and hid down in the bunker and waited for the mess to clear up! While I was down there, I worked on getting everything under my control! Once everything was done, I waited till you were long gone and began to reboot the systems!”
“What about the annihilator? Did you take control of it?”
“T-the what?!” Snively yelped, but squealed yet again when Shadow tugged on his hairs.
“ANSWER HIM!”
“I DON'T KNOW WHAT YOU'RE TALKING ABOUT! I SWEAR!” he screamed.
Sonic and Shadow looked at each other in suspicion and concern before Sonic looked back to Snively. “The Ultimate Annihilator? The weapon that Robuttnik was working on?”
“What are you talking about? He didn't have any such weapon!” Snively responded with terrorized confusion.
Sonic and Shadow looked at each other again before something came across Shadow's mind and looked back to Snively. “How did Sonic take out the Doctor then?”
“S-Sonic had gotten the chaos emeralds back from Uncle Julian while on the Death Egg, and took him and the station out!”
Shadow looked at Sonic again, who looked bewildered before looking to Snively. “That can't be right, I took out the Death Egg six months ago, and that wasn't what happened at all!”
“I think I know what's going on,” Shadow said, before letting go of Snively and shoving him in the chair. “Stay. Call SWATbots and I will destroy you.” he warned him before turning to Sonic. “Remember when I appeared yesterday? There was that temporal storm. It must of lingered and messed with the timeline here.”
Sonic looked spaced out for a moment, deep in thought. Shadow touched his arm. “Sonic?”
Sonic jolted slightly, looking at Shadow. “Sorry. Was thinking...just that...why wasn't Knothole affected if that was the case?”
Shadow had to think for a moment before Sonic suddenly answered his own question. “Oh wait. I remember something about the Annihilator affecting Knothole to where its in its own time zone or something like that. Three hours ahead of the rest of the world.”
“Oh, you're right. I wonder if the temporal storm affected the timeline because of the presence of that time bubble? Mixing time stuff? I'm not exactly a temporal mechanics expert.”
Sonic turned and walked over to the computer nearby. “Maybe I can get some information about what the world is currently like.”
As Sonic started typing furiously on the computer, Snively spoke up. “You'll never be able to get access to those computers. I encrypted the system with a security key so complicated that not even your-”
“-I'm in,” Sonic said as he began to look up information.
Shadow did a double-take while Snively yelped. “BUT THAT'S NOT POSSIBLE!!!”
“Sounds like you're really bad at security,” Shadow merely said as Sonic sifted through information.
Sonic looked back every now and again. “Yeah it looks like the timeline has really been muddled. Technically, Knothole isn't even in the system.”
Shadow looked to Sonic and came over to look at the computer screen. “If Knothole doesn't exist, where are the Freedom Fighters SUPPOSED to be?”
Sonic shook his head as he searched. “Some pockets of resistance within the city, but the only thing out in the Great Forest that Robotnik's been looking for and failed so far is some place called 'Sanctuary'. I'm now wondering if that's the area where Knothole now is.”
“Maybe we better make a copy of this information to take back to Knothole. Sally's going to want to know about this, I'm sure,” Shadow suggested.
“Way ahead of you. I'm trying now to see if I can network with Nicole and transmit the information,” Sonic responded.
Shadow looked to Sonic, surprised. “You can do that?”
“Actually...yeah-” he suddenly stopped, lifted his hands up, and looked to Shadow. “...why do I suddenly know about computers and how they work? I never understood any of this before now!”
Shadow frowned. “Get back to sending the transmission, we'll worry about that later.”
Sonic nodded and started typing again. Shadow watched the screen in thought. “I wonder if the time changes are starting to affect you.”
“I don't think so. Something in my gut tells me its something else,” Sonic said, looking frustrated at the computer. “Do you feel any different?”
Shadow paused for a moment in thought. “...no. But then again, I'm the cause of the temporal changes. Maybe I'm immune from it.”
“We'll have to check it out back at home. But right now, it looks like we won't be able to link to Nicole from here. I can't connect,” Sonic said, pulling away. “I think its because of the time bubble over Knothole, the time differences is interfering with the signal.”
“Sounds like we need to get back and get Sally to bring Nicole out here,” Shadow said, starting to turn around. “Meanwhile we can take-”
Looking behind him, Shadow noticed that the chair was empty. “Shit, the little fucker got away!”
Sonic looked back at him before pulling away from the computer. “Time to go then!”
He grabbed Shadow's hand and began to take off running, just as alarms began to sound. “Dammit, I should have been paying attention to the twerp!” Shadow grunted.
“Do you always swear?” Sonic asked as they ran down the hall, the sound of robots marching down from behind to find them.
“Does it really matter?” Shadow responded as they made it to the door leading out. He opened it, only to immediately shut it when lasers started shooting at them. “FUCK.”
Sonic looked around, trying to think. “When I say so, open the door and hide behind it. ”
Shadow looked back and ducked as SWATbots came around and started shooting at them. “You sure about this?”
“Trust me,” Sonic responded as Shadow reached up for the door. “NOW!”
Shadow flung the door open and ducked behind it with Sonic. With lasers firing outside and inside, the two parties of SWATbots were caught in the crossfire, shooting each other out. When they fell, the two hedgehogs peeked out from behind the door.
“That was quick thinking,” Shadow said.
“When am I not quick?” Sonic grinned cheekily before headed out the door. “Come on, we'd better get out of the city before more reinforcements come this way.”
The two hedgehogs ran through the city, forced to duck behind walls, into alleys, and behind garbage piles. Shadow grunted. “The twerp works quick. Every robot in the city must be on alert.”
“This is not gonna work,” Sonic muttered. “If we can get to my uncle's hideout, maybe we can stay there until the commotion blows over.”
Shadow nodded. “It's the best plan we got. Lead the way.”